This document provides a brief overview of the data, database organization and example queries. API database object names are in camel case. See the main API Documentation for more information on data models and query syntax.

The accompanying Allen Software Development Kit (SDK) provides python code for accessing electrophysiology data (NWB files) for all cells and morphological reconstructions (SWC files) for a subset of cells. The Allen SDK also provides sample code demonstrating how to download neuronal model parameters and run your own simulations using stimuli for the experiments or custom current injections.

Experimental Overview And Metadata

Each brain specimen is sectioned in the coronal plane at section thickness of 350 µm. The sections are then hemisected along the midline and a single cell in the hemisected tissue is targeted for electrophysiological recording and biocytin fill to visualize the cell morphology. Each cell is represented as Specimen object.

Each cell Specimen is associated with an anatomical Structure and CellSomaLocation record containing the coordinate of the cell in the Common Coordinate Framework and a normalized depth between pia (value of 0) and white matter (value of 1) surfaces.

Each cell Specimen is also associated with two SpecimenTags describing the “dendrite type” (spiny, aspiny, sparsely spiny) and the “apical dendrite” (intact, truncated, n/a).

Electrophysiology

All cells in the Allen Cell Types Database have electrophysiological recordings of responses to stimuli from a common set of current injection protocols. See the electrophysiology technical whitepaper for details on specimen selection, tissue processing, recording, and quality control.

The Cell Types Database categorizes detailed stimulus protocols into set of high level descriptions:

A ramp current injection with a slope of 25 pA/s is delivered, then terminated after the neuron fires a short series of action potentials.

Ramp to Rheobase

1 s pink noise epochs created using two different random seeds riding on top of a ramp transitioning to a plateau. The ramp portion of the stimulus is 14 seconds long. The noise on the ramp consists of alternating seeds all with a CV of .01. The noise on the plateau are organized into periods of six seconds containing noise of three different CV's with increasing and decreasing CV at 0.2, 0.4, 0.6, 0.4, and 0.2. After a period is completed using one random seed, the other random seed is played for a total of three periods.

Noise 1

Pink noise with a coefficient of variation (CV) equal to 0.2 is used to as it resembles in vivo data. These stimuli consist of 3 x 3 s noise epochs riding on top of square pulses at 0.75, 1, and 1.5 times rheobase. Recovery intervals between stimuli are 5 s.

Noise 2

Noise 1, with a different random seed

Test

General protocols used for testing experiment status

Stimulus sweeps that pass quality control standards are available for download as Neurodata Without Borders (NWB) files. To find the NWB download link for Rorb cell specimen 320654829, use this query:

The Allen SDK provides a simple Python module to support downloading metadata and NWB files for cells in the Cell Types Database. Please see the Data API Client documentation page to see an example.

A standard set of electrophysiological features are automatically computed from the recorded responses of each cell. A subset of those features are displayed at the top of the electrophysiology page for a cell:

Feature

Description

Upstroke:downstroke ratio

The average ratio between the absolute values of the action potential peak upstroke (i.e. max dV/dt) and the action potential peak downstroke (i.e. min dV/dt) for "Short Square" pulses.

Fast AP trough

Minimum value of the membrane potential in the interval lasting 5 ms after the peak of the first action potential for the minimum amplitude "Long Square" stimulus that elicited an action potential.

Morphology

The Allen Cell Types Database contains morphological reconstructions generated from bright-field images of biocytin-stained cells. Reconstructions are generated by manually curating the results of an automated segmentation algorithm. See the morphology technical whitepaper for more details.

A standard set of morphological features were computed for all reconstructed cells. A subset of those features are displayed at the top of the cell-specific morphology page:

Feature Name

Description

Max Euclidean Distance

The maximum Euclidean distance of all nodes. Euclidean distance is the straight line distance from the soma (root) to the node.

Number of Stems

The number of stems attached to the soma. When the type of the node is not soma, it is labeled as a stem.

Number of Bifurcations

The number of bifurcations for the given input neuron. A bifurcation point has two daughters.

Average Contraction

The average ratio between Euclidean distance of a branch and its path length. Euclidean distance of a branch is the straight-line distance from the soma to the branch. Path length is the sum of the lengths between each node along the path.

Parent:Daughter

The average ratio between the diameter of a daughter branch and its parent branch. One value for each daughter branch is generated at each bifurcation point.

See the morphology technical morphology technical whitepaper for a complete list of computed morphological features.

The API provides programmatic access to the microscopy images used for reconstruction, axis-oriented projections of those images, and morphological reconstructions. A cell can have up to four axis-oriented projections of the images used for reconstruction:

XY minimum intensity projection

YZ minimum intensity projection

XY maximum intensity projection

YZ maximum intensity projection

The reconstruction images display a dark, biocytin-filled cell on a light background. The maximum intensity projections are constructed from inverted and contrast-enhanced versions of the morphology images, resulting in a light cell on a dark background.

Single Cell Neuronal Models

The Allen Cell Types Database contains two types of neuronal models: perisomatic biophysical models and generalized leaky integrate-and-fire (GLIF) models. These models attempt to mathematically reproduce a cell's recorded response to a current injection. The perisomatic biophysical models take into account dendritic morphological structure, whereas GLIF models are simple point neuron models which represent the neuron as a single compartment.

There are five levels of GLIF models with increasing levels of complexity. The most basic model is a simple leaky integrate-and-fire equation. More advanced GLIFs attempt to model variable spike threshold, afterspike currents, and threshold adaptation.

Model Name

Description

1 Leaky Integrate and Fire (LIF)

Standard circuit representation of a resistor and capacitor in parallel with a leaky membrane.

2 LIF + Reset Rules (LIF-R)

LIF with biologically-derived threshold and voltage reset rules in addition to a biologically derived threshold decay.

All of the above, with an additional voltage-dependent component of threshold.

Biophysical, perisomatic

Models with active conductances at the soma and passive dendritic morphology based on full 3D reconstruction.

See the perisomatic biophysical and GLIF technical whitepapers for more details on how these models were created.

A cell's electrophysiology page displays all available models. Choose a model to see its simulated response to all stimuli presented to the cell. If the required sweeps are available, two model evaluation metrics are computed per model:

Metric Name

Required Sweeps

Description

Explained Variance Ratio

Noise 2 (at least two)

For "Noise 2" sweeps, the ratio of the mean explained variance of model spike times vs. experimental spike times to experiment-only mean explained variance.

Feature Average

Sweeps used for biophysical model fitting

Average absolute z-score comparing average spike features computed on model responses for sweeps used for fitting to spike features computed on experimental responses.

After selecting a model for display, the models ID number and a link for downloading necessary to run the model are available. For example, the link to download model 472427473 (a LIF model for Scnn1a cell 467703703) looks like this:

http://api.brain-map.org/neuronal_model/download/472427473

All models in the Allen Cell Types Database are available for download and local execution via the Allen Software Development Kit (SDK). The biophysical models require NEURON to be run, which the SDK helps to configure. The GLIF simulation module comes as part of the Allen SDK. Please visit the Allen SDK page for more details.